RNAi microarray analysis in cultured mammalian cells. Academic Article uri icon


  • RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) is a powerful new tool for analyzing gene knockdown phenotypes in living mammalian cells. To facilitate large-scale, high-throughput functional genomics studies using RNAi, we have developed a microarray-based technology for highly parallel analysis. Specifically, siRNAs in a transfection matrix were first arrayed on glass slides, overlaid with a monolayer of adherent cells, incubated to allow reverse transfection, and assessed for the effects of gene silencing by digital image analysis at a single cell level. Validation experiments with HeLa cells stably expressing GFP showed spatially confined, sequence-specific, time- and dose-dependent inhibition of green fluorescence for those cells growing directly on microspots containing siRNA targeting the GFP sequence. Microarray-based siRNA transfections analyzed with a custom-made quantitative image analysis system produced results that were identical to those from traditional well-based transfection, quantified by flow cytometry. Finally, to integrate experimental details, image analysis, data display, and data archiving, we developed a prototype information management system for high-throughput cell-based analyses. In summary, this RNAi microarray platform, together with ongoing efforts to develop large-scale human siRNA libraries, should facilitate genomic-scale cell-based analyses of gene function.

published proceedings

  • Genome Res

altmetric score

  • 4

author list (cited authors)

  • Mousses, S., Caplen, N. J., Cornelison, R., Weaver, D., Basik, M., Hautaniemi, S., ... Kallioniemi, O.

citation count

  • 171

complete list of authors

  • Mousses, Spyro||Caplen, Natasha J||Cornelison, Robert||Weaver, Don||Basik, Mark||Hautaniemi, Sampsa||Elkahloun, Abdel G||Lotufo, Roberto A||Choudary, Ashish||Dougherty, Edward R||Suh, Ed||Kallioniemi, Olli

publication date

  • October 2003